Journal: Molecular Brain

Article Title: Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue

doi: 10.1186/s13041-020-00584-7

Figure Lengend Snippet: Validation of Rab39b KO mice and monoclonal antibodies. a PCR analysis of Rab39b expression in brain tissue from two independent founder strains confirms complete KO of Rab39b and retained expression of Rab39a and Gapdh . b Evaluation of the specificity of RAB39B antibodies 12,162–1-AP (Proteintec), 1B8 and 1H1 by western blot analysis of human control and RAB39B KO tissue (derived from embryonic stem cell line MEL-1) and mouse wildtype and Rab39b KO tissue

Article Snippet: Quantitative real time PCR (qRT-PCR) analysis was performed with a LightCycler LC480 II (Roche) and taqman probes (Life Technologies) specific for mouse Rab39b (Mm00838519_m1) and Tbp (Mm00446971_m1).

Techniques: Biomarker Discovery, Bioprocessing, Expressing, Western Blot, Control, Derivative Assay

Journal: Molecular Brain

Article Title: Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue

doi: 10.1186/s13041-020-00584-7

Figure Lengend Snippet: Analysis of RAB39B by RT-PCR and western blot. a Quantification of Rab39b expression relative to Tbp in whole mouse brain from 2 weeks to 12 month of age (mean ± SEM, n = 3 per time point). b Representative western blot of steady state RAB39B in whole mouse brain from 2 weeks to 12 month of age. c Quantification of RAB39B steady state levels relative to β-Actin in whole mouse brain from 2 weeks to 12 month of age (mean ± SEM, n = 3 per time point). d Representative western blot of steady state RAB39B in micro-dissected mouse brain ( n = 3 per tissue region). e Quantification of RAB39B steady state levels relative to β-Actin in micro-dissected mouse brain (mean ± SEM, n = 3)

Article Snippet: Quantitative real time PCR (qRT-PCR) analysis was performed with a LightCycler LC480 II (Roche) and taqman probes (Life Technologies) specific for mouse Rab39b (Mm00838519_m1) and Tbp (Mm00446971_m1).

Techniques: Reverse Transcription Polymerase Chain Reaction, Western Blot, Expressing

Journal: Molecular Brain

Article Title: Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue

doi: 10.1186/s13041-020-00584-7

Figure Lengend Snippet: Distribution of Rab39b by ISH in mouse brain tissue. Representative images of Rab39b localization by ISH in coronal sections of 1 month old mouse brain ( n = 3) at Bregma coordinates ( a ) -1.70 mm, ( b ) -2.30 mm and ( c ) -2.80 mm. Scale bar = 500 μm. ( d - g ) High magnification images of Rab39b localization by ISH at the ( d ) hippocampus, ( e ) cortex, ( f ) caudate putamen and ( g ) SN. Scale bar = 100 μm

Article Snippet: Quantitative real time PCR (qRT-PCR) analysis was performed with a LightCycler LC480 II (Roche) and taqman probes (Life Technologies) specific for mouse Rab39b (Mm00838519_m1) and Tbp (Mm00446971_m1).

Techniques:

Journal: Molecular Brain

Article Title: Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue

doi: 10.1186/s13041-020-00584-7

Figure Lengend Snippet: Distribution of RAB39B by IHC in mouse brain tissue. Representative images of RAB39B localization by IHC in coronal sections of 1 month old mouse brain ( n = 3) at the a cerebral cortex co-stained with MAP2, b , c hippocampus co-stained with MAP2, d SN co-stained with TH, e caudate putamen co-stained with MAP2 and f thalamus co-stained with MAP2. Boxed areas in upper panels (scale bar = 200 μm) are shown at a higher magnification in the corresponding lower panels (scale bar = 50 μm)

Article Snippet: Quantitative real time PCR (qRT-PCR) analysis was performed with a LightCycler LC480 II (Roche) and taqman probes (Life Technologies) specific for mouse Rab39b (Mm00838519_m1) and Tbp (Mm00446971_m1).

Techniques: Staining

Journal: Frontiers in Neurology

Article Title: Genetic Analysis of RAB39B in an Early-Onset Parkinson's Disease Cohort

doi: 10.3389/fneur.2020.00523

Figure Lengend Snippet: Depiction of sequencing and copy number variant analyses performed for RAB39B in this study (black text) and previously (gray text) of an early-onset Parkinson's disease cohort. The three variants identified in the study are indicated.

Article Snippet: We performed an analysis of RAB39B CNV by quantitative real-time PCR (RT-PCR), utilizing commercially available Taqman assays interrogating exon 1, exon 2, or the 3′UTR of RAB39B (Life Technologies, Hs00817269_cn, Hs00745075_cn, and Hs02637133_cn, respectively; ).

Techniques: Sequencing, Variant Assay

Journal: Frontiers in Neurology

Article Title: Genetic Analysis of RAB39B in an Early-Onset Parkinson's Disease Cohort

doi: 10.3389/fneur.2020.00523

Figure Lengend Snippet: In silico analyses of the 5′ region of RAB39B . (A) Screenshot of the UCSC browser (hg38, chrX:155,264,156-155,264,850) examining the 5′ region of RAB39B . The location of the chrX:154493802-C-T variant is depicted by the red dotted line. The blue sequences represent Refseq NM_171998.3 (outdated) and NM_171998.4, respectively. Spliced human expressed sequence tags are shown in black. The lower tracks demonstrate that the variant is located within a region of DNase 1 sensitivity and displays high vertebrate conservation compared to immediate flanking sequence. The final track demonstrating GERP scores represents an analysis of the corresponding sequence using the hg19 dataset. (B) An alignment of the 5′ region of RAB39B showing the reference genomic sequence (top) with the variant sequence (middle). The predicted AP-1 transcription factor binding site is in bold highlight. The sequence logo (bottom) generated from ENCODE data demonstrates the core AP-1 consensus sequence and the conservation of each nucleotide.

Article Snippet: We performed an analysis of RAB39B CNV by quantitative real-time PCR (RT-PCR), utilizing commercially available Taqman assays interrogating exon 1, exon 2, or the 3′UTR of RAB39B (Life Technologies, Hs00817269_cn, Hs00745075_cn, and Hs02637133_cn, respectively; ).

Techniques: In Silico, Variant Assay, Sequencing, Binding Assay, Generated

Journal: Frontiers in Neurology

Article Title: Genetic Analysis of RAB39B in an Early-Onset Parkinson's Disease Cohort

doi: 10.3389/fneur.2020.00523

Figure Lengend Snippet: Depiction of sequencing and copy number variant analyses performed for RAB39B in this study (black text) and previously (gray text) of an early-onset Parkinson's disease cohort. The three variants identified in the study are indicated.

Article Snippet: We performed an analysis of RAB39B CNV by quantitative real-time PCR (RT-PCR), utilizing commercially available Taqman assays interrogating exon 1, exon 2, or the 3′UTR of RAB39B (Life Technologies, Hs00817269_cn, Hs00745075_cn, and Hs02637133_cn, respectively; ).

Techniques: Sequencing, Variant Assay

Journal: Frontiers in Neurology

Article Title: Genetic Analysis of RAB39B in an Early-Onset Parkinson's Disease Cohort

doi: 10.3389/fneur.2020.00523

Figure Lengend Snippet: In silico analyses of the 5′ region of RAB39B . (A) Screenshot of the UCSC browser (hg38, chrX:155,264,156-155,264,850) examining the 5′ region of RAB39B . The location of the chrX:154493802-C-T variant is depicted by the red dotted line. The blue sequences represent Refseq NM_171998.3 (outdated) and NM_171998.4, respectively. Spliced human expressed sequence tags are shown in black. The lower tracks demonstrate that the variant is located within a region of DNase 1 sensitivity and displays high vertebrate conservation compared to immediate flanking sequence. The final track demonstrating GERP scores represents an analysis of the corresponding sequence using the hg19 dataset. (B) An alignment of the 5′ region of RAB39B showing the reference genomic sequence (top) with the variant sequence (middle). The predicted AP-1 transcription factor binding site is in bold highlight. The sequence logo (bottom) generated from ENCODE data demonstrates the core AP-1 consensus sequence and the conservation of each nucleotide.

Article Snippet: We performed an analysis of RAB39B CNV by quantitative real-time PCR (RT-PCR), utilizing commercially available Taqman assays interrogating exon 1, exon 2, or the 3′UTR of RAB39B (Life Technologies, Hs00817269_cn, Hs00745075_cn, and Hs02637133_cn, respectively; ).

Techniques: In Silico, Variant Assay, Sequencing, Binding Assay, Generated